Detailed kinetic analysis and identification of the nucleophile in alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase

J Biol Chem. 2002 Nov 15;277(46):43667-73. doi: 10.1074/jbc.M208285200. Epub 2002 Sep 6.

Abstract

alpha-l-Arabinofuranosidases cleave the l-arabinofuranoside side chains of different hemicelluloses and are key enzymes in the complete degradation of the plant cell wall. The alpha-l-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase, was subjected to a detailed mechanistic study. Aryl-alpha-l-arabinofuranosides with various leaving groups were synthesized and used to verify the catalytic mechanism and catalytic residues of the enzyme. The steady-state constants and the resulting Brønsted plots for the E175A mutant are consistent with the role of Glu-175 as the acid-base catalytic residue. The proposed nucleophile residue, Glu-294, was replaced to Ala by a double-base pairs substitution. The resulting E294A mutant, with 4-nitrophenyl alpha-l-arabinofuranoside as the substrate, exhibited eight orders of magnitude lower activity and a 10-fold higher K(m) value compared with the wild type enzyme. Sodium azide accelerated by more than 40-fold the rate of the hydrolysis of 2',4',6'-trichlorophenyl alpha-l-arabinofuranoside by the E294A mutant. The glycosyl-azide product formed during this reaction was isolated and characterized as beta-l-arabinofuranosyl-azide by (1)H NMR, (13)C NMR, mass spectrometry, and Fourier transform infrared analysis. The anomeric configuration of this product supports the assignment of Glu-294 as the catalytic nucleophile residue of the alpha-l-arabinofuranosidase T-6 and allows for the first time the unequivocal identification of this residue in glycoside hydrolases family 51.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alanine / chemistry
  • Azides / pharmacology
  • Bacillaceae / enzymology*
  • Catalytic Domain
  • Cell Wall / metabolism
  • Chromatography, Thin Layer
  • Cloning, Molecular
  • Dose-Response Relationship, Drug
  • Geobacillus stearothermophilus / enzymology*
  • Glutamic Acid / chemistry
  • Glycoside Hydrolases / chemistry*
  • Glycoside Hydrolases / metabolism*
  • Hydrogen-Ion Concentration
  • Hydrolysis
  • Kinetics
  • Magnetic Resonance Spectroscopy
  • Mass Spectrometry
  • Models, Chemical
  • Mutagenesis, Site-Directed
  • Sodium Azide / pharmacology
  • Spectroscopy, Fourier Transform Infrared
  • Time Factors

Substances

  • Azides
  • Glutamic Acid
  • Sodium Azide
  • Glycoside Hydrolases
  • alpha-N-arabinofuranosidase
  • Alanine